AIMC Topic: Protein Transport

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Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

G3 (Bethesda, Md.) May 5, 2017
High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a ta...
Machine Learning Proteome Yeasts Fungal Proteins Protein Transport Microscopy, Fluorescence High-Throughput Screening Assays Image Interpretation, Computer-Assisted
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Identifying the missing proteins in human proteome by biological language model.

BMC systems biology Dec 23, 2016
BACKGROUND: With the rapid development of high-throughput sequencing technology, the proteomics research becomes a trendy field in the post genomics era. It is necessary to identify all the native-encoding protein sequences for further function and p...
Intracellular Space Protein Transport Gene Ontology Proteomics Proteome Models, Theoretical Databases, Protein Natural Language Processing Probability Humans
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Sorting protein decoys by machine-learning-to-rank.

Scientific reports Aug 17, 2016
Much progress has been made in Protein structure prediction during the last few decades. As the predicted models can span a broad range of accuracy spectrum, the accuracy of quality estimation becomes one of the key elements of successful protein str...
Machine Learning Models, Molecular Algorithms Protein Transport Proteins
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Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction.

Bioinformatics (Oxford, England) Apr 23, 2016
MOTIVATION: Bioimages of subcellular protein distribution as a new data source have attracted much attention in the field of automated prediction of proteins subcellular localization. Performance of existing systems is significantly limited by the sm...
Algorithms Computational Biology Bayes Theorem Humans Fluorescent Antibody Technique Organelles Supervised Machine Learning Immunohistochemistry Protein Transport
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Multiplex protein pattern unmixing using a non-linear variable-weighted support vector machine as optimized by a particle swarm optimization algorithm.

Talanta Oct 21, 2015
Most of the proteins locate more than one organelle in a cell. Unmixing the localization patterns of proteins is critical for understanding the protein functions and other vital cellular processes. Herein, non-linear machine learning technique is pro...
Protein Transport Algorithms Support Vector Machine Microscopy, Fluorescence
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Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble.

BMC bioinformatics Aug 25, 2015
BACKGROUND: It has become a very important and full of challenge task to predict bacterial protein subcellular locations using computational methods. Although there exist a lot of prediction methods for bacterial proteins, the majority of these metho...
Intracellular Space Gram-Positive Bacteria Bacterial Proteins Protein Transport Gram-Negative Bacteria Gene Ontology
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Identification of novel Xanthomonas euvesicatoria type III effector proteins by a machine-learning approach.

Molecular plant pathology Aug 15, 2015
The Gram-negative bacterium Xanthomonas euvesicatoria (Xcv) is the causal agent of bacterial spot disease in pepper and tomato. Xcv pathogenicity depends on a type III secretion (T3S) system that delivers effector proteins into host cells to suppress...
Bacterial Secretion Systems Base Composition Machine Learning Plant Cells Phylogeny Xanthomonas Plant Leaves Capsicum Plant Diseases Bacterial Proteins Nicotiana Protein Transport Mutation
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TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.

Bioinformatics (Oxford, England) Jun 16, 2015
MOTIVATION: Molecular recognition of N-terminal targeting peptides is the most common mechanism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can...
Machine Learning Software Peptides Chloroplasts Support Vector Machine Mitochondria Sequence Analysis, Protein Protein Transport Mitochondrial Proteins Eukaryota Chloroplast Proteins
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Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

PloS one Apr 20, 2015
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
Biological Ontologies Protein Transport Molecular Sequence Annotation Humans Signal Transduction Toll-Like Receptors Animals Evolution, Molecular Mice Computational Biology Chickens
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Protein submitochondrial localization from integrated sequence representation and SVM-based backward feature extraction.

Molecular bioSystems Oct 21, 2014
Mitochondrion, a tiny energy factory, plays an important role in various biological processes of most eukaryotic cells. Mitochondrial defection is associated with a series of human diseases. Knowledge of the submitochondrial locations of proteins can...
Protein Transport Models, Biological Mitochondria Datasets as Topic Support Vector Machine Reproducibility of Results Proteins Colorectal Neoplasms ROC Curve Humans Algorithms
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